On Tue, Feb 15, 2011 at 10:43 AM, Shannon Quinn <[email protected]> wrote:
Hi Shannon, > > > It would be interesting to see how the current implementation can be > > integrated into your Bioinformatics course work, what extensions you > > need for this particular domain. > > I assume your HMM would be for the purpose of protein/nucleic acid sequence > analysis and alignment. HMMs/MDPs are fairly domain-independent, but this > would definitely be an interesting pursuit; I'm a grad student in comp bio, > and I know a lot of folks who would love to use this. > Yes, I'm interested in applying HMMs for protein sequence analysis, and seeing if they can be applied to predict the side chain conformation of protein sequences on large data sets using Mahout. The following paper uses a HMM in form of a Dynamic Bayesian Network for the same purpose: http://www.biomedcentral.com/1471-2105/11/306 It will be interesting to extend Mahout's existing HMM code so that it could be distributed over large clusters. I'm working with a professor here at UMass on side chain structure prediction as well this semester and he said that we can craft out a nice, tight proposal for this purpose for GSoC. Dhruv > > On the topic of GSoC, I meant to mention: I'm happy to volunteer my > services as a potential mentor for the summer. > > Shannon > > Apologies for the brevity, this was sent from my iPhone
